AMBER Archive (2008)

Subject: Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Fri Jul 04 2008 - 01:33:03 CDT

Also, when you use "Readmerge" to read ClusterMerging.txt generated by
averagelinkage, does PairwiseDistances file have to be present? If not, will
Readmerge re-calculate PairwiseDistances?

Thanks,

-DX

On Thu, Jul 3, 2008 at 11:28 PM, Dong Xu <d1xu_at_ucsd.edu> wrote:

> Hi Jianyin,
>
> I see there's an option [verbose *verb*]. Could you tell me how to use.
> The clustering manual didn't mention it at all.
>
> Thanks,
>
> -DX
>
>
> On Fri, May 30, 2008 at 10:11 AM, Jianyin Shao <jyshao2004_at_gmail.com>
> wrote:
> >
> >
> >>
> >> I understand that "X" labels the correspondent frames to the cluster
> >> members. I wrote a python script to translate "X" to frame number. But
> >> what I wanted to know was how to obtain or extract the frame numbers
> >> for the cluster representatives in "filename.rep.ci" files.
> >
> > One "dumb" trick you may try is to use the representative structure as
> > reference and run rms fitting for the entire trajectory. The one with
> rmsd
> > of 0 should be the representative frame.
> >>
> >> Since ptraj already has "rms" command, rms fitting in clustering seems
> >> a bit redundant if "rms" command is explicitly required prior to
> >> running "cluster" command.
> >
> > The rms command will fit to a specific structure. In clustering, the
> > structures in the trajectory will be aligned to different representative
> > structures of clusters to obtain reasonable centroids.
> >
> >
> > Good luck,
> >
> > Jianyin
> >
> >
>
>

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